Morpho-physiological screenings and molecular analysis of west sumatra rice genotypes under submergence stress

Abstract

This study investigates the submergence tolerance level of 14 rice genotypes by morpho-physiological and molecular analyses of Sub1 alleles. IR64-Sub1 was used as a submergence tolerant check. The submergence screenings were conducted by submerging 14-days-old seedlings in water tanks for 14 days while molecular analysis was conducted using 14 Sub1 linked markers. The results showed that 5 tested genotypes, namely Inpari 48 Blas, Mundam Putiah, Batang Piaman, Banang Pulau and Pulau Sijunjung, recorded high survival rates (SR) of 80% to 100% under submergence stress. PCR-based identification of the Sub1 alleles confirmed that several tested genotypes carry Sub1A and Sub1C, but not all were expressed in their phenotypic performance towards submergence. IR64-Sub1 and Batang Piaman not only showed well-adaptation towards submergence by maintaining lower elongation (<20%) and less chlorophyll content change (TCC) (<30%) but were also equipped with the Sub1A allele. These genotypes potentially provide good phenotypic and genotypic performance under submergence stress conditions. Additionally, based on population structure analysis, these genotypes were grouped into 3 clusters, of which 35.71% are pure accessions, while the remaining 64.29% have admixture ancestry between populations 1, 2 and 3. The data in model-based population structure and UPGMA dendrogram supported that rice genotypes in this study have 3 well-differentiated genetic populations and admixtures. Most genotypes have a close genetic relationship with Nei’s similarity index ranging from 0.571 to 0.893.